Anchor points for genome alignment based on Filtered Spaced Word Matches

Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as anchor points to reduce the search space of the alignment procedure. Speed and quality of these methods therefore depend on the underlying anchor points. Herein, we propose to use Filtered Spaced Word Matches to calculate anchor points for genome alignment. To evaluate this approach, we used these anchor points in the the widely used alignment pipeline Mugsy. For distantly related sequence sets, we could substantially improve the quality of alignments produced by Mugsy.